Replace tabix module

CHANGELOG.md

@@ -16,10 +16,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Adding nf-core HAPPY_REPORT module to generate a standalone interactive HTML report from the stratified hap.py results (`*.roc.all.csv.gz`) of all test VCFs, for germline small variant benchmarks. [#326](https://github.com/nf-core/variantbenchmarking/pull/326)
 - `happy_comparison_engine` parameter to choose the hap.py comparison engine (`default`, `xcmp`, `vcfeval`). The `scmp-somatic` and `scmp-distance` engines are not supported because of unresolved issues in hap.py ([Illumina/hap.py#181](https://github.com/Illumina/hap.py/issues/181)). The chosen engine is also passed to HAPPY_REPORT as `comparison_method`. [#327](https://github.com/nf-core/variantbenchmarking/pull/327)
 - hap.py now uses a Seqera container that bundles RTG Tools, so `--happy_comparison_engine vcfeval` works without a custom container. The `test_ga4gh` profile now uses the parameter instead of a process override. [#327](https://github.com/nf-core/variantbenchmarking/pull/327)
+- Replace nf-core modules TABIX_TABIX, TABIX_BGZIP and TABIX_BGZIPTABIX with HTSLIB_BGZIPTABIX [#328](https://github.com/nf-core/variantbenchmarking/pull/328).
 
 ### `Fixed`
 
-- Depreciated HAPPY_PREPY: new versions of happy uses prepy integration, normalization functions for prepy can be provided through happy args. [#316](https://github.com/nf-core/variantbenchmarking/issues/313).
+- Deprecated HAPPY_PREPY: new versions of happy uses prepy integration, normalization functions for prepy can be provided through happy args. [#316](https://github.com/nf-core/variantbenchmarking/issues/313).
 - Fixing metromap to light to dark background. Adding docs/images/metro_map.md to assist future developers to reproduce the metromap. [#316](https://github.com/nf-core/variantbenchmarking/pull/316).
 - Update happy module to use both -R and -f arguments.[#319](https://github.com/nf-core/variantbenchmarking/pull/319)
 - Fixing regions_bed vs high_conf_bed confusion.[#319](https://github.com/nf-core/variantbenchmarking/pull/319)
@@ -31,13 +32,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency         | Old version | New version |
 | ------------------ | ----------- | ----------- |
-| pigz               | 2.8         | depreciated |
+| pigz               | 2.8         | deprecated  |
 | nf-core            | 3.5.1       | 4.1.0       |
 | prettier           | 3.6.2       | 3.8.3       |
-| prepy              | 0.3.15      | depreciated |
-| r-base             | 4.1.0       | depreciated |
+| prepy              | 0.3.15      | deprecated  |
+| r-base             | 4.1.0       | deprecated  |
 | ga4gh-happy-report | -           | 0.1.2       |
 | rtg-tools (hap.py) | -           | 3.13        |
+| tabix              | 1.21        | deprecated  |
+| htslib             | -           | 1.24        |
+| xz                 | -           | 5.8.3       |
 
 ## 1.5.0
 

conf/modules.config

@@ -26,6 +26,21 @@ process {
         ]
     }
 
+    withName: HTSLIB_BGZIPTABIX {
+        ext.prefix = { infile.name.replaceAll(/\.vcf\.gz$|\.vcf$|\.gz$/, "") }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: 'TABIX_BGZIPTABIX*' {
+        publishDir = [
+            path: {"${params.outdir}/${params.variant_type}/${meta.id}/preprocess"},
+            pattern: "*{.vcf.gz,vcf.gz.tbi}",
+            mode: params.publish_dir_mode
+        ]
+    }
+
     // subsample_vcf test
 
     withName: BCFTOOLS_SORT {
@@ -239,12 +254,6 @@ process {
         ]
     }
 
-    withName: TABIX_TABIX {
-        publishDir = [
-            enabled: false
-        ]
-    }
-
     withName: SURVIVOR_FILTER {
         ext.prefix = { vcf_file.baseName - ".vcf" + ".filter"}
         publishDir = [
@@ -320,14 +329,6 @@ process {
         ]
     }
 
-    withName: 'TABIX_BGZIPTABIX*' {
-        publishDir = [
-            path: {"${params.outdir}/${params.variant_type}/${meta.id}/preprocess"},
-            pattern: "*{.vcf.gz,vcf.gz.tbi}",
-            mode: params.publish_dir_mode
-        ]
-    }
-
     withName: BCFTOOLS_SORT_SV {
         ext.prefix = { vcf.baseName - ".vcf" + ".sort"}
         ext.args   = {"--output-type z --write-index=tbi" }
@@ -565,19 +566,6 @@ process {
         ]
     }
 
-    withName: "TABIX_BGZIP*"{
-        ext.prefix = {input.toString() - ".vcf.gz"}
-        publishDir = [
-            enabled: false
-        ]
-    }
-    withName: "TABIX_BGZIPTABIX*"{
-        ext.prefix = { input.baseName }
-        publishDir = [
-            enabled: false
-        ]
-    }
-
     withName: BCFTOOLS_VIEW_TRUTH {
         ext.prefix = {  vcf.baseName - ".vcf" + ".truth" }
         ext.args  = {"--output-type z --write-index=tbi -s TRUTH" }
@@ -684,13 +672,6 @@ process {
 
     // compare_benchmark_results
 
-    withName: TABIX_BGZIP_UNZIP{
-        ext.prefix = {input.toString() - ".vcf.gz"}
-        publishDir = [
-            enabled: false
-        ]
-    }
-
     withName: PLOTS_SVLEN_DIST {
         ext.prefix = {"${meta.id}.${meta.tag}"}
         publishDir = [

main.nf

@@ -16,8 +16,8 @@
 */
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_variantbenchmarking_pipeline'
 
-params.fasta = getGenomeAttribute('fasta')
-params.fai   = getGenomeAttribute('fai')
+params.fasta      = getGenomeAttribute('fasta')
+params.fai        = getGenomeAttribute('fai')
 params.dictionary = getGenomeAttribute('dict')
 
 /*
@@ -38,7 +38,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vari
 
 // WORKFLOW: Run main nf-core/variantbenchmarking analysis pipeline
 workflow NFCORE_VARIANTBENCHMARKING {
-
     take:
     samplesheet
 
@@ -47,13 +46,14 @@ workflow NFCORE_VARIANTBENCHMARKING {
     //
     // WORKFLOW: Run pipeline
     //
-    VARIANTBENCHMARKING (
+    VARIANTBENCHMARKING(
         samplesheet,
         params.multiqc_config,
         params.multiqc_logo,
         params.multiqc_methods_description,
         params.outdir,
     )
+
     emit:
     multiqc_report = VARIANTBENCHMARKING.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
@@ -65,12 +65,10 @@ workflow NFCORE_VARIANTBENCHMARKING {
 */
 
 workflow {
-
-    main:
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION (
+    PIPELINE_INITIALISATION(
         params.version,
         params.validate_params,
         params.monochrome_logs,
@@ -79,30 +77,24 @@ workflow {
         params.input,
         params.help,
         params.help_full,
-        params.show_hidden
+        params.show_hidden,
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_VARIANTBENCHMARKING (
+    NFCORE_VARIANTBENCHMARKING(
         PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    PIPELINE_COMPLETION (
+    PIPELINE_COMPLETION(
         params.email,
         params.email_on_fail,
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        NFCORE_VARIANTBENCHMARKING.out.multiqc_report
+        NFCORE_VARIANTBENCHMARKING.out.multiqc_report,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/

modules.json

@@ -101,6 +101,11 @@
                         "git_sha": "4020dbe4bb4a7d71be85bf8f77dbdf6c06fa401f",
                         "installed_by": ["modules"]
                     },
+                    "htslib/bgziptabix": {
+                        "branch": "master",
+                        "git_sha": "37f69c8ca3eb3d038a5d44f33a329e49f44bd4f2",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
@@ -176,21 +181,6 @@
                         "git_sha": "fdcc3976e728b5d6ffc3f15979905829531e6072",
                         "installed_by": ["modules"]
                     },
-                    "tabix/bgzip": {
-                        "branch": "master",
-                        "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db",
-                        "installed_by": ["modules"]
-                    },
-                    "tabix/bgziptabix": {
-                        "branch": "master",
-                        "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db",
-                        "installed_by": ["modules"]
-                    },
-                    "tabix/tabix": {
-                        "branch": "master",
-                        "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a",
-                        "installed_by": ["modules"]
-                    },
                     "truvari/bench": {
                         "branch": "master",
                         "git_sha": "fb32a7ee01805151ef9355fdee4bf035c727de24",